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Q9LTX3 (PPOX1_ARATH) Reviewed, UniProtKB/Swiss-Prot

Last modified June 11, 2014. Version 101. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Pyridoxine/pyridoxamine 5'-phosphate oxidase 1, chloroplastic

Short name=AtPPOX1

Including the following 2 domains:

  1. Pyridoxine/pyridoxamine 5'-phosphate oxidase
    EC=1.4.3.5
    Alternative name(s):
    PNP/PMP oxidase
    Short name=PNPOx
    Pyridoxal 5'-phosphate synthase
  2. Probable NAD(P)HX epimerase
    EC=5.1.99.-
Gene names
Name:PPOX1
Synonyms:PDX3, PDXH
Ordered Locus Names:At5g49970
ORF Names:K9P8.11
OrganismArabidopsis thaliana (Mouse-ear cress) [Reference proteome]
Taxonomic identifier3702 [NCBI]
Taxonomic lineageEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis

Protein attributes

Sequence length530 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Catalyzes the oxidation of either pyridoxine 5'-phosphate (PNP) or pyridoxamine 5'-phosphate (PMP) into pyridoxal 5'-phosphate (PLP). Involved in the PLP salvage pathway. Has a higher preference for PNP over PMP. May also catalyze the epimerization of the S- and R-forms of NAD(P)HX, a damaged form of NAD(P)H that is a result of enzymatic or heat-dependent hydration. This is a prerequisite for the S-specific NAD(P)H-hydrate dehydratase to allow the repair of both epimers of NAD(P)HX. Ref.5 Ref.6

Catalytic activity

Pyridoxamine 5'-phosphate + H2O + O2 = pyridoxal 5'-phosphate + NH3 + H2O2. Ref.5 Ref.6

Pyridoxine 5'-phosphate + O2 = pyridoxal 5'-phosphate + H2O2. Ref.5 Ref.6

(R)-NADHX = (S)-NADHX. Ref.5 Ref.6

Cofactor

Binds 1 FMN per subunit By similarity. HAMAP-Rule MF_01629

Binds 1 potassium ion per subunit By similarity. HAMAP-Rule MF_01629

Pathway

Cofactor biosynthesis; B6 vitamer interconversion; pyridoxal 5'-phosphate from pyridoxamine 5'-phosphate: step 1/1. HAMAP-Rule MF_01629

Cofactor biosynthesis; B6 vitamer interconversion; pyridoxal 5'-phosphate from pyridoxine 5'-phosphate: step 1/1.

Subunit structure

Homodimer By similarity. HAMAP-Rule MF_01629

Subcellular location

Plastidchloroplast Ref.7.

Tissue specificity

Expressed in leaves, stems, flowers and roots. Ref.7

Induction

Circadian regulation. Up-regulated by light, heat, jasmonic acid, ethylene and abscisic acid treatments. Down-regulated by drought and salt treatment. Not induced by UV irradiation. Ref.7

Domain

Most plant PPOX proteins have both a pyridoxamine 5'-phosphate oxidase domain and an extra YjeF N-terminal domain. HAMAP-Rule MF_01629

Miscellaneous

Mutants with reduced expression of PPOX1 (RNAi) have lower levels of total B6 vitamers, a reduced growth and are sensitive to high light (Ref.7).

Sequence similarities

In the N-terminal section; belongs to the NnrE/AIBP family.

In the C-terminal section; belongs to the pyridoxamine 5'-phosphate oxidase family.

Contains 1 YjeF N-terminal domain.

Sequence caution

The sequence AAM65907.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

The sequence AAM83249.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q9LTX3-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.
Isoform 2 (identifier: Q9LTX3-2)

The sequence of this isoform differs from the canonical sequence as follows:
     261-271: Missing.
     478-530: Missing.
Note: Not detected in roots.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Transit peptide1 – 6363Chloroplast Potential
Chain64 – 530467Pyridoxine/pyridoxamine 5'-phosphate oxidase 1, chloroplastic HAMAP-Rule MF_01629
PRO_0000420549

Regions

Domain81 – 297217YjeF N-terminal
Nucleotide binding389 – 3902FMN By similarity
Nucleotide binding453 – 4542FMN By similarity
Region131 – 1355NAD(P)HX By similarity
Region200 – 2067NAD(P)HX By similarity
Region321 – 3244Substrate binding By similarity
Region505 – 5073Substrate binding By similarity

Sites

Metal binding1321Potassium By similarity
Metal binding1961Potassium By similarity
Metal binding2411Potassium By similarity
Binding site2381NAD(P)HX By similarity
Binding site3741FMN By similarity
Binding site3771FMN; via amide nitrogen By similarity
Binding site3791Substrate By similarity
Binding site3961FMN By similarity
Binding site4361Substrate By similarity
Binding site4401Substrate By similarity

Natural variations

Alternative sequence261 – 27111Missing in isoform 2.
VSP_044534
Alternative sequence478 – 53053Missing in isoform 2.
VSP_044535

Experimental info

Sequence conflict2411S → Y in AAM65907. Ref.4

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified October 1, 2000. Version 1.
Checksum: 22E8DFEC1A2167EE

FASTA53059,376
        10         20         30         40         50         60 
MRNVIRRVTT MTFTFLLQSP PLPISPSPPQ FSLSSSPLSK TQRFITPSQG SRLRTLCTKV 

        70         80         90        100        110        120 
IIPNMQDSGS PPLSYLTQRE AAEIDETLMG PLGFSIDQLM ELAGLSVAAS IAEVYKPEEY 

       130        140        150        160        170        180 
SRVLAICGPG NNGGDGLVAA RHLHHFGYKP FICYPKRTAK PLYTGLVTQL DSLSVPFVSV 

       190        200        210        220        230        240 
EDLPDDLSKD FDVIVDAMFG FSFHGAPRPP FDDLIRRLVS LQNYEQTLQK HPVIVSVDIP 

       250        260        270        280        290        300 
SGWHVEEGDH EDGGIKPDML VSLTAPKLCA KRFRGPHHFL GGRFVPPSVA EKYKLELPSY 

       310        320        330        340        350        360 
PGTSMCVRIG KPPKVDISAM RVNYVSPELL EEQVETDPTV QFRKWFDEAV AAGLRETNAM 

       370        380        390        400        410        420 
ALSTANKDKK PSSRMVLLKG FDENGFVWFT NYESKKGSDL SENPSAALLF YWEILNRQVR 

       430        440        450        460        470        480 
IEGPVERIPE SESENYFHSR PRGSQIGAIV SKQSSVVPGR HVLYDEYEEL TKQYSDGSVI 

       490        500        510        520        530 
PKPKNWGGFR LKPNLFEFWQ GQPSRLHDRL QYSLQDVNGN PAWKIHRLAP 

« Hide

Isoform 2 [UniParc].

Checksum: 3E2B851F982461E5
Show »

FASTA46652,042

References

« Hide 'large scale' references
[1]"Structural analysis of Arabidopsis thaliana chromosome 5. X. Sequence features of the regions of 3,076,755 bp covered by sixty P1 and TAC clones."
Sato S., Nakamura Y., Kaneko T., Katoh T., Asamizu E., Kotani H., Tabata S.
DNA Res. 7:31-63(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: cv. Columbia.
[2]The Arabidopsis Information Resource (TAIR)
Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
Cited for: GENOME REANNOTATION.
Strain: cv. Columbia.
[3]"Empirical analysis of transcriptional activity in the Arabidopsis genome."
Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G. expand/collapse author list , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.
Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 12-530 (ISOFORM 1).
Strain: cv. Columbia.
[4]"Full-length cDNA from Arabidopsis thaliana."
Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B., Feldmann K.A.
Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 34-530 (ISOFORM 1).
[5]"Identification of a pyridoxine (pyridoxamine) 5'-phosphate oxidase from Arabidopsis thaliana."
Sang Y., Barbosa J.M., Wu H., Locy R.D., Singh N.K.
FEBS Lett. 581:344-348(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION AS PYRIDOXINE/PYRIDOXAMINE 5'-PHOSPHATE OXIDASE, CATALYTIC ACTIVITY.
[6]"Vitamer levels, stress response, enzyme activity, and gene regulation of Arabidopsis lines mutant in the pyridoxine/pyridoxamine 5'-phosphate oxidase (PDX3) and the pyridoxal kinase (SOS4) genes involved in the vitamin B6 salvage pathway."
Gonzalez E., Danehower D., Daub M.E.
Plant Physiol. 145:985-996(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION AS PYRIDOXINE/PYRIDOXAMINE 5'-PHOSPHATE OXIDASE, CATALYTIC ACTIVITY.
[7]"Expression, in vivo localization and phylogenetic analysis of a pyridoxine 5'-phosphate oxidase in Arabidopsis thaliana."
Sang Y., Locy R.D., Goertzen L.R., Rashotte A.M., Si Y., Kang K., Singh N.K.
Plant Physiol. Biochem. 49:88-95(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: TISSUE SPECIFICITY, INDUCTION, ALTERNATIVE SPLICING, SUBCELLULAR LOCATION.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AB024032 Genomic DNA. Translation: BAA97018.1.
CP002688 Genomic DNA. Translation: AED95879.1.
CP002688 Genomic DNA. Translation: AED95878.1.
AY127025 mRNA. Translation: AAM83249.1. Different initiation.
BT000605 mRNA. Translation: AAN18174.1.
AY088368 mRNA. Translation: AAM65907.1. Different initiation.
RefSeqNP_568717.2. NM_124376.3. [Q9LTX3-1]
NP_974918.1. NM_203189.1. [Q9LTX3-2]
UniGeneAt.28155.

3D structure databases

ProteinModelPortalQ9LTX3.
SMRQ9LTX3. Positions 73-309, 337-530.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING3702.AT5G49970.1-P.

Proteomic databases

PRIDEQ9LTX3.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsAT5G49970.1; AT5G49970.1; AT5G49970. [Q9LTX3-1]
GeneID835061.
KEGGath:AT5G49970.

Organism-specific databases

TAIRAT5G49970.

Phylogenomic databases

eggNOGCOG0259.
HOGENOMHOG000243404.
InParanoidQ9LTX3.
KOK00275.
K17759.
OMACVRIGKP.
PhylomeDBQ9LTX3.

Enzyme and pathway databases

BioCycARA:AT5G49970-MONOMER.
MetaCyc:MONOMER-17901.
UniPathwayUPA00190; UER00304.
UPA00190; UER00305.

Gene expression databases

GenevestigatorQ9LTX3.

Family and domain databases

Gene3D2.30.110.10. 1 hit.
3.40.50.10260. 1 hit.
HAMAPMF_01629. PdxH.
MF_01966. NADHX_epimerase.
InterProIPR000659. Pyridox_Oxase.
IPR019740. Pyridox_Oxase_CS.
IPR011576. Pyridox_Oxase_FMN-bd.
IPR021198. Pyridox_Oxase_pln.
IPR019576. Pyridoxamine_oxidase_dimer_C.
IPR012349. Split_barrel_FMN-bd.
IPR004443. YjeF_N_dom.
[Graphical view]
PfamPF10590. PNPOx_C. 1 hit.
PF01243. Pyridox_oxidase. 1 hit.
PF03853. YjeF_N. 1 hit.
[Graphical view]
PIRSFPIRSF037048. PyrdxN_5-P_Oxase_ross-cont_pln. 1 hit.
SUPFAMSSF50475. SSF50475. 1 hit.
SSF64153. SSF64153. 1 hit.
TIGRFAMsTIGR00558. pdxH. 1 hit.
TIGR00197. yjeF_nterm. 1 hit.
PROSITEPS01064. PYRIDOX_OXIDASE. 1 hit.
PS51385. YJEF_N. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry namePPOX1_ARATH
AccessionPrimary (citable) accession number: Q9LTX3
Secondary accession number(s): F4K7H2, Q8L7T7, Q8L9L3
Entry history
Integrated into UniProtKB/Swiss-Prot: January 9, 2013
Last sequence update: October 1, 2000
Last modified: June 11, 2014
This is version 101 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PATHWAY comments

Index of metabolic and biosynthesis pathways

Arabidopsis thaliana

Arabidopsis thaliana: entries and gene names